
That was funny!!!! I have to have a look to the file when have time!
The reason of shape order bronken is that maybe the scripts are called AFTER the internal bone dynamics routine is called (maybe before) and the position of the bones are not the correct one. I don't know...
If you did not realize yet, the 3D position of each point is given by the relative coordinates of the Rx (for the x coordinate) and Ry (for the y and z coordinates) bones. The position is relative to its parent (in the most basic case the first bone you create and the rotation center). If you include other bones between that rotation center bone and the Rx and/or Ry bones, then the 3D coordinates are broken.
What you can do is create some limbs and include bone dynamic to the mX and mY bones. It would respect the 3D coordinates and always be coherent.
I hope next week I could finish the tutorials (In fact, I haven't started them jet

By the way I think the basic tutorial I'm preparing wouldn't give you new clues. I think you have the main concepts already learned!

Best
-G